Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India

Rangaiah, Ambica; Shankar, Sathyanarayan Muthur; Padukone, Shashiraja; Rangappa, Kusuma Gowdra; Basawarajappa, Shantala Gowdara

doi:10.1128/mra.00850-21

Cited by 2 publications

(1 citation statement)

References 5 publications

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“…In the United States, two high-frequency mutations, L84S and S24L, were discovered [83]. I121L was observed in asymptomatic Indian individuals [100].…”

Section: Orf8 Proteinmentioning

confidence: 99%

Analysis of Whole-Genome Sequencing of SARS-CoV-2 Reveals Recurrent Mutations among Iranian Patients

Abbasian

Mahdavi

Mahmanzar

et al. 2022

Preprint

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BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new emerging coronavirus that causes coronavirus disease 2019 (COVID-19). Whole-genome tracking of the SARS-CoV-2 enhanced our understanding of the mechanism of disease, control, and prevent COVID-19 infections.Materials and MethodsIn the current study, we investigated 1221 SARS-CoV-2 protein sequences of Iranian SARS-CoV-2 in the public database of the GISAID from January 2019 to April 2022. Prepare a list of suitable samples and preprocess performed by python programming language. To compare and identify mutation patterns SARS-CoV-2 genome was aligned to the Wuhan-Hu-1 as a reference sequence.ResultsOur investigation revealed that spike-P323L, ORF9c-G50N, NSP14-I42V, spike-D614G, NSP4-T492I, nucleocapsid-R203K, nucleocapsid-G204R, membrane-A63T, membrane-Q19E, NSP5-P132H, envelope-T9I, NSP3-G489S, ORF3a-T24I, membrane-D3G, spike-S477N, Spike-D478K, nucleocapsid-S235F, spike-N501Y, nucleocapsid-D3L, and spike-P861H as the most frequent mutations among the Iranian SARS-COV-2 sequences. Furthermore, it was observed that more than 95 % of the SARS-CoV-2 genome, including NSP7, NSP8, NSP9, NSP10, NSP11, and ORF8, had no mutation when compared to the Wuhan-Hu-1. Finally, our data indicated the ORF3a-T24I, NSP3-G489S, NSP5-P132H, NSP14-I42V, envelope-T9I, nucleocapsid-D3L, membrane-Q19E, and membrane-A63T mutations might be one of the responsible factors for the surge in the SARS-CoV-2 omicron variant wave in Iran.DiscussionOur results highlight the value of real-time genomic surveillance that help to identify novel SARS-CoV-2 variants and could be applied to update SARS-CoV-2 diagnostic tools, vaccine design, and understanding of the mechanisms of adaptation to a new host environment.

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“…In the United States, two high-frequency mutations, L84S and S24L, were discovered [83]. I121L was observed in asymptomatic Indian individuals [100].…”

Section: Orf8 Proteinmentioning

confidence: 99%

Analysis of Whole-Genome Sequencing of SARS-CoV-2 Reveals Recurrent Mutations among Iranian Patients

Abbasian

Mahdavi

Mahmanzar

et al. 2022

Preprint

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Comparative Atlas of SARS-CoV-2 Substitution Mutations: A Focus on Iranian Strains Amidst Global Trends

Abbasian,

Rahimian,

Mahmanzar

et al. 2024

Viruses

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Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new emerging coronavirus that caused coronavirus disease 2019 (COVID-19). Whole-genome tracking of SARS-CoV-2 enhanced our understanding of the mechanism of the disease, control, and prevention of COVID-19. Methods: we analyzed 3368 SARS-CoV-2 protein sequences from Iran and compared them with 15.6 million global sequences in the GISAID database, using the Wuhan-Hu-1 strain as a reference. Results: Our investigation revealed that NSP12-P323L, ORF9c-G50N, NSP14-I42V, membrane-A63T, Q19E, and NSP3-G489S were found to be the most frequent mutations among Iranian SARS-CoV-2 sequences. Furthermore, it was observed that more than 94% of the SARS-CoV-2 genome, including NSP7, NSP8, NSP9, NSP10, NSP11, and ORF8, had no mutations when compared to the Wuhan-Hu-1 strain. Finally, our data indicated that the ORF3a-T24I, NSP3-G489S, NSP5-P132H, NSP14-I42V, envelope-T9I, nucleocapsid-D3L, membrane-Q19E, and membrane-A63T mutations might be responsible factors for the surge in the SARS-CoV-2 Omicron variant wave in Iran. Conclusions: real-time genomic surveillance is crucial for detecting new SARS-CoV-2 variants, updating diagnostic tools, designing vaccines, and understanding adaptation to new environments.

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Whole-Genome Sequencing of SARS-CoV-2 Strains from Asymptomatic Individuals in India

Cited by 2 publications

References 5 publications

Analysis of Whole-Genome Sequencing of SARS-CoV-2 Reveals Recurrent Mutations among Iranian Patients

Analysis of Whole-Genome Sequencing of SARS-CoV-2 Reveals Recurrent Mutations among Iranian Patients

Comparative Atlas of SARS-CoV-2 Substitution Mutations: A Focus on Iranian Strains Amidst Global Trends

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